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I built R 3.6.0 from source on Redhat 7 and added the path, initiate it as shown below.

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"

Now I try to install the packages for e.g install.packages("BiocManager"), which I can do this with the earlier versions of R but not with 3.6.0. I get the error. 

mv: cannot move '/home/a/R/lib64/R/library/00LOCK-BiocManager/00new/BiocManager' to '/home/a/R/lib64/R/library/BiocManager': File exists
ERROR:   moving to final location failed
* removing '/home/a/R/lib64/R/library/BiocManager'

The downloaded source packages are in
        '/tmp/RtmpQsq3KA/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("BiocManager") :
  installation of package 'BiocManager' had non-zero exit status

Though, I am not sure about the error.

AwaitedOne
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  • Well, what flags did you set when you complied R? The error says that `/home/a/R/lib64/R/library/BiocManager` already exists. Does it already exist? Did a previous install fail? What if you remove that and try installing it again? – MrFlick May 29 '19 at 15:40
  • @MrFlick, Thank you for your comment. I did `./configure --prefix=$HOME/R` and then `make && make install`. `BiocManager` does not already exist. I get the error for every package I try to install. – AwaitedOne May 29 '19 at 15:59
  • Appears issue with moving location. Perhaps check admin privileges. – CT Hall May 29 '19 at 17:02
  • I see the error is with `R .3.6.0` – AwaitedOne May 29 '19 at 20:54
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    We were getting this too with a similar build. There is a solution here:https://stackoverflow.com/questions/56241007/non-zero-exit-status-r-3-6-0-biobase?noredirect=1&lq=1 Sys.setenv(R_INSTALL_STAGED = FALSE) After setting this I can now install Rmpi – Andrew Lewis Jun 07 '19 at 09:36

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